Objective This randomized clinical trial investigated the effects of adding cervico-mandibular manual therapies into an exercise and educational program on clinical outcomes in individuals with tinnitus associated with temporomandibular disorders (TMDs). Methods Sixty-one patients with tinnitus attributed to TMD were randomized into the physiotherapy and manual therapy group or physiotherapy alone group. All patients received six sessions of physiotherapy treatment including cranio-cervical and temporomandibular joint (TMJ) exercises, self-massage, and patient education for a period of one month. Patients allocated to the manual therapy group also received cervico-mandibular manual therapies targeting the TMJ and cervical and masticatory muscles. Primary outcomes included TMD pain intensity and tinnitus severity. Secondary outcomes included tinnitus-related handicap (Tinnitus Handicap Inventory [THI]), TMD-related disability (Craniofacial Pain and Disability Inventory [CF-PDI]), self-rated quality of life (12-item Short Form Health Survey [SF-12]), depressive symptoms (Beck Depression Inventory [BDI-II]), pressure pain thresholds (PPTs), and mandibular range of motion. Patients were assessed at baseline, one week, three months, and six months after intervention by a blinded assessor. Results The adjusted analyses showed better outcomes (all, P < 0.001) in the exercise/education plus manual therapy group (large effect sizes) for TMD pain (η 2 P = 0.153), tinnitus severity (η 2 P = 0.233), THI (η 2 P = 0.501), CF-PDI (η 2 P = 0.395), BDI-II (η 2 P = 0.194), PPTs (0.363 < η 2 P < 0.415), and range of motion (η 2 P = 0.350), but similar changes for the SF-12 (P = 0.622, η 2 P = 0.01) as the exercise/education alone group. Conclusions This clinical trial found that application of cervico-mandibular manual therapies in combination with exercise and education resulted in better outcomes than application of exercise/education alone in individuals with tinnitus attributed to TMD.